HowTo install AliEn from source


HowTo upgrade to a new AliEn version


HowTo get debug output

Add "-- debug 5" at the end of the alien call e.g.

"alien login --debug 5"

HowTo add a post install file

This has to be done before the package is added

  • Create a proxy
    • alien proxy-init
  • Login to alien
    • alien login
    • The user is defined . $HOME?.alien/Environment
  • Goto directory where you want to add the file. If the directory don't exist create the directory
    • e.g. mkdir -p packages/panda_extern/0.1
    • e.g. cd packages/panda_extern/0.1
  • Add the file to the file catalog
    • add [filename] [file location on local computer]
    • e.g. add post_install /misc/uhlig/post_install

HowTo add a package

This add the new package to the file catalog

  • Define the package you want to install
    • packman define [name] [version] [file location on local computer] post_install=[location of postinstall file] -platform source -se [SE] -dependencies="list of dependencies"
    • e.g. packman define panda_extern 0.1 /misc/uhlig/cbmsoft_devel_021107.tar.gz post_install=/panda/user/p/pbarprod/packages/panda_extern/0.1/post_install
    • packman define pandaroot 0.4 /misc/uhlig/SVN/ctest/test/pandaroot_r1727.tar.gz dependencies=panda_extern::0.1 post_install=/panda/user/p/pbarprod/packages/pandaroot/0.4/postinstall
    • packman define cbmroot jun09 /misc/cbmgrid/alien_packages/cbmroot/cbmroot_jun09.tar.gz dependencies=cbm_extern::jul08 post_install=/cbm/user/c/cbmgrid/packages/cbmroot/jun09/cbmroot_postinstall_jun09 -platform source -se CBM::GSI::xrdlustre
In the directory there now should be two files post_install and Linux-i686. If there is no difference between i686 and x86_64 copy Linux-i686 to Linux-x86_64. This is normaly correct if you deal with source packages which are compiled on the grid computers. After this step you should be prepared for everything.

HowTo remove a package

  • packman undefine [name] [version] -platform [source][i686][x86_64]

Normally this is done automatically when you submit a job which depends on some packages. But for testing it can be done in a manual fassion

  • Install the package on a dedicate site (CE Computing Element)
    • packman install [package]::[version] [site]
    • e.g. packman install panda_extern::0.1 PANDA::GSI::grid8

HowTo get information about a package

  • packman list -force
  • packman test package
    • packman test cbmroot::dec10
  • packman listInstalled -name [packman instance of this site]
    • packman listInstalled -name CBM::GSI::lxi020_packman

Short tutorial for using Alien

  • Login on as user cbmgrid
  • Check certificate and if expired create new one
    • alien proxy-info
    • alien proxy-init
  • Login to the alien system
    • alien login
  • Move to jdl directory
    • cd jdl
  • View and describe date1.jdl and date2.jdl
    • cat date1.jdl
  • Submit a job to the grid
    • submit date1.jdl
  • Check job status
    • top (to show all processes)
    • ps trace id (show complete info about process id)
    • ps trace id all (show more verbose output about the job)
    • masterJob id (show status of all subjobs of the masterjob)
    • masterjob id -status status resubmit (resubmit all subjobs which ended in status)
  • Check the output of job with id
    • cat /proc/cbmgrid//job-output/stdout
  • Submit a job with parameters (5)
    • submit dat1.jdl 5
  • Check what the job is doing while execution. The first command shows the files in the workdir. The second command shows the last of the standard output.
    • spy <id> workdir
    • spy <id> stdout tail <nr_of_lines> 

HowTo update/change a host certificate

  • Download the certificate from your CA authority
  • Export the certificate from the browser (Browser dependent)
  • Extract the certificate (public key) into PEM-format. The requested password is the password you defined during the export from the browser.
    • openssl pkcs12 -clcerts -nokeys -in mycert.p12 -out usercert.pem
  • Extract the certificate (private key) into PEM-format. The requested password is the password you defined during the export from the browser. It is important that no passphrase is defined because of the machine certificate.
    • openssl pkcs12 -in mykey.pem -nocerts -nodes -out hostkey.pem
  • Copy the newly created certificates into the right directories
  • Central services
    • hostkey.pem -> ~/.alien/globus/userkey.pem
    • hostkey.pem -> ~/.alien/etc/aliend/ldap/certs/host.key.pem
    • hostkey.pem -> /etc/aliend/ldap/certs/hostkey.pem
    • usercert.pem -> ~/.alien/globus/usercert.pem
    • usercert.pem -> ~/.alien/etc/aliend/ldap/certs/host.cert.pem
    • usercert.pem -> /etc/aliend/ldap/certs/hostcert.pem
  • Site services
    • hostkey.pem -> ~/.alien/globus/userkey.pem
    • usercert.pem -> ~/.alien/globus/usercert.pem

Problems with file quotas

If you see a error message like below it could be that the user exceeds the file quotas.

 Job 1982 inserted from 
 Job state transition from INSERTING to WAITING
 Job state transition to STARTED    |=|  procinfotime: 1292241432 site: CBM::GSI::lxcbmgrid001_ce started: 1292241432
 Job state transition from STARTED    to RUNNING    |=|  procinfotime: 1292241432 site: CBM::GSI::lxcbmgrid001_ce 
                                        started: 1292241432 spyurl: node: 
 Job state transition from RUNNING    to SAVING     |=|  procinfotime: 1292241432 site: CBM::GSI::lxcbmgrid001_ce 
 Job state transition to ERROR_SV   |=|  procinfotime: 1292241442 site: CBM::GSI::lxcbmgrid001_ce 
                                     spyurl:  finished: 1292241442 
 ENVELOPE ERROR: Uploading file for user (cbmgrid) is denied, file size (727) - total file size quota exceeded.
 Authen has thrown an access exception: [quotaexception]
 Could not store the file /tmp/cbmgrid-work/alien-job-1982/log_archive on any SE. This file is lost!
 The job finished on the worker node with status ERROR_SV

The file quotas can be changed by the admin. The command to see the quotas is

fquota list -unit G

The command to set the quotas is

fquota set <user> maxTotalSize <size in Bytes>

to set the maximum number of bytes to be used by the user. To set the maximum number of files the command is

fquota set <user> maxNbFiles <number of files>

-- FlorianUhlig - 05 Nov 2007
Topic revision: r19 - 2011-06-08, FlorianUhlig
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